Multiple sequence alignment - TraesCS6B01G129800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)



BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G129800 chr6B 100.000 4908 0 0 1 4908 126216882 126221789 0.000000e+00 9064.0
1 TraesCS6B01G129800 chr6B 89.452 1441 143 8 1886 3323 126629833 126631267 0.000000e+00 1810.0
2 TraesCS6B01G129800 chr6B 90.538 539 48 2 1 536 41378377 41378915 0.000000e+00 710.0
3 TraesCS6B01G129800 chr6B 82.511 223 23 6 1685 1891 449292723 449292501 1.090000e-41 182.0
4 TraesCS6B01G129800 chr6D 95.451 2374 71 19 2043 4411 56020647 56022988 0.000000e+00 3751.0
5 TraesCS6B01G129800 chr6D 88.843 1452 144 13 1886 3326 56275357 56276801 0.000000e+00 1768.0
6 TraesCS6B01G129800 chr6D 88.630 1029 61 19 609 1603 56019214 56020220 0.000000e+00 1201.0
7 TraesCS6B01G129800 chr6D 89.514 391 31 2 2865 3245 62244002 62243612 2.050000e-133 486.0
8 TraesCS6B01G129800 chr6D 88.591 298 14 4 1607 1884 56020251 56020548 1.310000e-90 344.0
9 TraesCS6B01G129800 chr6D 76.140 570 76 35 710 1236 56273980 56274532 1.360000e-60 244.0
10 TraesCS6B01G129800 chr6A 94.428 2315 79 19 1889 4184 70571016 70573299 0.000000e+00 3515.0
11 TraesCS6B01G129800 chr6A 90.110 1365 122 11 1972 3326 70911812 70913173 0.000000e+00 1760.0
12 TraesCS6B01G129800 chr6A 91.017 1013 69 10 609 1603 70569457 70570465 0.000000e+00 1347.0
13 TraesCS6B01G129800 chr6A 87.708 301 11 10 1607 1883 70570503 70570801 1.320000e-85 327.0
14 TraesCS6B01G129800 chr6A 94.737 95 3 1 4191 4285 70574657 70574749 3.960000e-31 147.0
15 TraesCS6B01G129800 chr6A 98.718 78 1 0 4334 4411 70574751 70574828 6.620000e-29 139.0
16 TraesCS6B01G129800 chr6A 86.275 102 10 3 4808 4908 112606472 112606374 1.870000e-19 108.0
17 TraesCS6B01G129800 chr7B 98.512 605 7 1 1 603 693836993 693836389 0.000000e+00 1066.0
18 TraesCS6B01G129800 chr7B 96.640 506 10 1 4410 4908 41518534 41519039 0.000000e+00 833.0
19 TraesCS6B01G129800 chr2B 98.512 605 7 1 1 603 194644427 194643823 0.000000e+00 1066.0
20 TraesCS6B01G129800 chr2B 89.312 683 54 8 2648 3320 23365379 23366052 0.000000e+00 839.0
21 TraesCS6B01G129800 chr2B 95.059 506 15 3 4411 4908 462919953 462920456 0.000000e+00 787.0
22 TraesCS6B01G129800 chr2B 94.702 151 7 1 4411 4560 462919753 462919903 2.950000e-57 233.0
23 TraesCS6B01G129800 chr5B 96.812 596 15 3 1 593 271040433 271041027 0.000000e+00 992.0
24 TraesCS6B01G129800 chr4D 95.586 589 24 1 1 587 497421055 497421643 0.000000e+00 942.0
25 TraesCS6B01G129800 chr4D 95.676 555 22 1 1 553 497414089 497414643 0.000000e+00 891.0
26 TraesCS6B01G129800 chr4D 90.492 589 30 7 1 587 497438167 497438731 0.000000e+00 754.0
27 TraesCS6B01G129800 chr4D 90.186 591 29 5 1 587 497417633 497418198 0.000000e+00 743.0
28 TraesCS6B01G129800 chr4D 90.039 512 26 2 1 510 497424657 497425145 1.490000e-179 640.0
29 TraesCS6B01G129800 chr2D 89.286 588 38 6 1 586 618134304 618134868 0.000000e+00 713.0
30 TraesCS6B01G129800 chr2D 85.897 156 18 3 4753 4908 469887768 469887919 3.930000e-36 163.0
31 TraesCS6B01G129800 chr3B 90.891 505 33 7 4413 4908 222141505 222142005 0.000000e+00 665.0
32 TraesCS6B01G129800 chr3B 86.922 497 32 16 4414 4908 790740828 790741293 1.210000e-145 527.0
33 TraesCS6B01G129800 chr5A 86.907 443 31 15 1889 2330 121943023 121942607 5.750000e-129 472.0
34 TraesCS6B01G129800 chr5A 86.682 443 29 17 1889 2330 123291790 123291377 9.620000e-127 464.0
35 TraesCS6B01G129800 chr5A 85.779 443 37 17 1889 2330 519494577 519494160 3.490000e-121 446.0
36 TraesCS6B01G129800 chr5A 83.908 174 12 1 1734 1891 121943259 121943086 8.510000e-33 152.0
37 TraesCS6B01G129800 chr5A 83.908 174 12 1 1734 1891 123292026 123291853 8.510000e-33 152.0
38 TraesCS6B01G129800 chr5A 93.617 47 1 2 1843 1887 490406473 490406427 8.820000e-08 69.4
39 TraesCS6B01G129800 chr2A 89.628 376 30 2 2865 3232 659628980 659628606 2.070000e-128 470.0
40 TraesCS6B01G129800 chr2A 88.747 391 34 2 2865 3245 735655915 735655525 2.070000e-128 470.0
41 TraesCS6B01G129800 chr7D 90.785 293 22 5 2049 2339 19643191 19643480 2.140000e-103 387.0
42 TraesCS6B01G129800 chr1B 91.829 257 18 2 4652 4908 581700874 581700621 6.040000e-94 355.0
43 TraesCS6B01G129800 chr1B 84.400 250 22 8 4568 4802 389317221 389316974 3.820000e-56 230.0
44 TraesCS6B01G129800 chr1D 79.562 411 57 13 4411 4797 287618658 287618251 8.100000e-68 268.0
45 TraesCS6B01G129800 chr4B 80.172 232 20 11 1677 1891 592868612 592868390 3.060000e-32 150.0
46 TraesCS6B01G129800 chr3A 91.489 47 2 2 1843 1887 148996326 148996280 4.100000e-06 63.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G129800 chr6B 126216882 126221789 4907 False 9064.000000 9064 100.000000 1 4908 1 chr6B.!!$F2 4907
1 TraesCS6B01G129800 chr6B 126629833 126631267 1434 False 1810.000000 1810 89.452000 1886 3323 1 chr6B.!!$F3 1437
2 TraesCS6B01G129800 chr6B 41378377 41378915 538 False 710.000000 710 90.538000 1 536 1 chr6B.!!$F1 535
3 TraesCS6B01G129800 chr6D 56019214 56022988 3774 False 1765.333333 3751 90.890667 609 4411 3 chr6D.!!$F1 3802
4 TraesCS6B01G129800 chr6D 56273980 56276801 2821 False 1006.000000 1768 82.491500 710 3326 2 chr6D.!!$F2 2616
5 TraesCS6B01G129800 chr6A 70911812 70913173 1361 False 1760.000000 1760 90.110000 1972 3326 1 chr6A.!!$F1 1354
6 TraesCS6B01G129800 chr6A 70569457 70574828 5371 False 1095.000000 3515 93.321600 609 4411 5 chr6A.!!$F2 3802
7 TraesCS6B01G129800 chr7B 693836389 693836993 604 True 1066.000000 1066 98.512000 1 603 1 chr7B.!!$R1 602
8 TraesCS6B01G129800 chr7B 41518534 41519039 505 False 833.000000 833 96.640000 4410 4908 1 chr7B.!!$F1 498
9 TraesCS6B01G129800 chr2B 194643823 194644427 604 True 1066.000000 1066 98.512000 1 603 1 chr2B.!!$R1 602
10 TraesCS6B01G129800 chr2B 23365379 23366052 673 False 839.000000 839 89.312000 2648 3320 1 chr2B.!!$F1 672
11 TraesCS6B01G129800 chr2B 462919753 462920456 703 False 510.000000 787 94.880500 4411 4908 2 chr2B.!!$F2 497
12 TraesCS6B01G129800 chr5B 271040433 271041027 594 False 992.000000 992 96.812000 1 593 1 chr5B.!!$F1 592
13 TraesCS6B01G129800 chr4D 497414089 497425145 11056 False 804.000000 942 92.871750 1 587 4 chr4D.!!$F2 586
14 TraesCS6B01G129800 chr4D 497438167 497438731 564 False 754.000000 754 90.492000 1 587 1 chr4D.!!$F1 586
15 TraesCS6B01G129800 chr2D 618134304 618134868 564 False 713.000000 713 89.286000 1 586 1 chr2D.!!$F2 585
16 TraesCS6B01G129800 chr3B 222141505 222142005 500 False 665.000000 665 90.891000 4413 4908 1 chr3B.!!$F1 495
17 TraesCS6B01G129800 chr5A 121942607 121943259 652 True 312.000000 472 85.407500 1734 2330 2 chr5A.!!$R3 596
18 TraesCS6B01G129800 chr5A 123291377 123292026 649 True 308.000000 464 85.295000 1734 2330 2 chr5A.!!$R4 596


AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
708 7679 0.534412 CGAGACTTGACCCAGAGCAT 59.466 55.0 0.0 0.0 0.00 3.79 F
1293 8320 0.101399 CGTCTGGTTCGGATCTCTGG 59.899 60.0 0.0 0.0 0.00 3.86 F
1308 8335 0.117140 TCTGGGAGATCTGTGGGTGT 59.883 55.0 0.0 0.0 0.00 4.16 F
2905 10543 0.625849 AATGGGAGGCACCGAAGATT 59.374 50.0 0.0 0.0 40.11 2.40 F
3709 11355 0.026803 CTGCTATTTTCGACGCCTGC 59.973 55.0 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2593 10229 0.107945 CTTTGCTCTTCTCCTCCCCG 60.108 60.000 0.00 0.0 0.00 5.73 R
2974 10616 0.527565 CATGCCACTTGCCCTTGTAC 59.472 55.000 0.00 0.0 40.16 2.90 R
3296 10941 5.880054 AATGTACGGAAAACATCAGAAGG 57.120 39.130 0.00 0.0 36.56 3.46 R
3857 11505 0.321653 GCGGTTGTGTCATCCTCCTT 60.322 55.000 0.00 0.0 0.00 3.36 R
4556 13576 4.008933 GCTGCAGGAGGTCGTGGT 62.009 66.667 17.12 0.0 32.80 4.16 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
603 7573 1.541588 GGGTGTGACAAGGCAAATCTC 59.458 52.381 0.00 0.00 0.00 2.75
604 7574 1.197721 GGTGTGACAAGGCAAATCTCG 59.802 52.381 0.00 0.00 0.00 4.04
605 7575 2.143122 GTGTGACAAGGCAAATCTCGA 58.857 47.619 0.00 0.00 0.00 4.04
606 7576 2.158449 GTGTGACAAGGCAAATCTCGAG 59.842 50.000 5.93 5.93 0.00 4.04
607 7577 1.129437 GTGACAAGGCAAATCTCGAGC 59.871 52.381 7.81 0.00 0.00 5.03
690 7661 3.316573 GAGTGGGTGAAGGGAGGCG 62.317 68.421 0.00 0.00 0.00 5.52
708 7679 0.534412 CGAGACTTGACCCAGAGCAT 59.466 55.000 0.00 0.00 0.00 3.79
725 7696 1.202463 GCATGCATCTACGTGGAGTCT 60.202 52.381 14.21 0.00 0.00 3.24
758 7729 2.281484 GTCACCACGCCCACATGT 60.281 61.111 0.00 0.00 0.00 3.21
763 7734 2.048222 CACGCCCACATGTCGTCT 60.048 61.111 7.99 0.00 33.84 4.18
771 7742 2.009774 CCACATGTCGTCTTCCCATTC 58.990 52.381 0.00 0.00 0.00 2.67
778 7749 1.361668 CGTCTTCCCATTCGCCACAG 61.362 60.000 0.00 0.00 0.00 3.66
801 7773 3.049080 GCCCGGGAGCCTCTGATTT 62.049 63.158 29.31 0.00 0.00 2.17
988 7984 2.725008 GCAGAGAGATCGGGTCGG 59.275 66.667 0.00 0.00 0.00 4.79
991 7987 2.195139 GAGAGATCGGGTCGGGGA 59.805 66.667 0.00 0.00 0.00 4.81
1114 8135 2.048222 TCCGGTTCTTCGCTGCTG 60.048 61.111 0.00 0.00 0.00 4.41
1150 8176 2.867429 CGAGATTTGTGATGGTTTGCC 58.133 47.619 0.00 0.00 0.00 4.52
1168 8195 0.465287 CCTGGGTTTTGCAGCTGTTT 59.535 50.000 16.64 0.00 0.00 2.83
1216 8243 4.361971 AGCTGGGTCGTCTCCGGA 62.362 66.667 2.93 2.93 32.49 5.14
1268 8295 0.178987 ACCTCTCTCGTGTGGACTGT 60.179 55.000 0.00 0.00 0.00 3.55
1274 8301 0.941463 CTCGTGTGGACTGTGTGCTC 60.941 60.000 0.00 0.00 0.00 4.26
1285 8312 2.022129 GTGTGCTCGTCTGGTTCGG 61.022 63.158 0.00 0.00 0.00 4.30
1290 8317 0.248702 GCTCGTCTGGTTCGGATCTC 60.249 60.000 0.00 0.00 0.00 2.75
1293 8320 0.101399 CGTCTGGTTCGGATCTCTGG 59.899 60.000 0.00 0.00 0.00 3.86
1308 8335 0.117140 TCTGGGAGATCTGTGGGTGT 59.883 55.000 0.00 0.00 0.00 4.16
1353 8432 1.134220 TGAGGTGGTGAAACGCTTCTT 60.134 47.619 0.00 0.00 38.12 2.52
1411 8490 4.342092 TGATGATGAATTAGGAGCGAGACA 59.658 41.667 0.00 0.00 0.00 3.41
1438 8517 3.306088 GCTGCTCAACTGTCCTAGTGTTA 60.306 47.826 0.00 0.00 40.26 2.41
1441 8520 4.184629 GCTCAACTGTCCTAGTGTTATGG 58.815 47.826 0.00 0.00 40.26 2.74
1465 8544 6.008331 GGATCCAAAACATATAACCCTACCC 58.992 44.000 6.95 0.00 0.00 3.69
1533 8658 1.949631 GATACTAGGCACGCCGCAC 60.950 63.158 1.61 0.00 45.17 5.34
1603 8761 9.477484 GTTTTGAGAAGTGAACTGACTATCTTA 57.523 33.333 0.00 0.00 0.00 2.10
1604 8762 9.698309 TTTTGAGAAGTGAACTGACTATCTTAG 57.302 33.333 0.00 0.00 0.00 2.18
1627 8832 4.173256 CAGTTGAACTGGGTTTGAAACAC 58.827 43.478 17.27 6.90 42.35 3.32
1666 8871 6.173339 CACAATTATACTAGTAGGCCCATGG 58.827 44.000 4.14 4.14 0.00 3.66
1745 8955 6.707608 TCCTCAACCATCTGAAATATTCATCG 59.292 38.462 0.00 0.00 39.30 3.84
1751 8961 8.539770 ACCATCTGAAATATTCATCGTATGAC 57.460 34.615 0.00 0.00 39.39 3.06
1848 9102 9.638239 GATTAAAACTGTTGCTCCAAATGATAA 57.362 29.630 0.00 0.00 0.00 1.75
1887 9141 7.275999 GCGCCTAGCTCTTAATTACCTTAATAG 59.724 40.741 0.00 0.00 44.04 1.73
1993 9517 2.084546 CTGTGTTAAACCTAGGCCTGC 58.915 52.381 17.99 0.00 0.00 4.85
1995 9519 2.907696 TGTGTTAAACCTAGGCCTGCTA 59.092 45.455 17.99 0.00 0.00 3.49
2005 9529 3.629398 CCTAGGCCTGCTATTCTTTGTTG 59.371 47.826 17.99 0.00 0.00 3.33
2040 9664 3.592427 TCCCAGGTCTTCTCTACTGTAGT 59.408 47.826 14.11 0.00 0.00 2.73
2084 9715 2.029020 TGTCTGACTCCATTTCCTGTCG 60.029 50.000 9.51 0.00 32.64 4.35
2160 9796 5.471116 TGATATAAATCTGTGATGCAGGTGC 59.529 40.000 0.00 0.00 45.08 5.01
2275 9911 3.561313 GCCCTGTTACTTTGAAGGATGGA 60.561 47.826 0.00 0.00 30.92 3.41
2548 10184 7.309928 CCATATGACAAGCTCTCTCATGTCTAT 60.310 40.741 13.56 8.82 42.03 1.98
2593 10229 3.564225 ACGAGGTCAGAATTTTGGTTGAC 59.436 43.478 0.00 0.00 39.29 3.18
2905 10543 0.625849 AATGGGAGGCACCGAAGATT 59.374 50.000 0.00 0.00 40.11 2.40
3296 10941 6.317391 CCTTTCTGAGTTCCAGGTAATTCATC 59.683 42.308 0.00 0.00 43.12 2.92
3411 11056 5.597813 AGATCTTCAGCGTTTTGTACAAG 57.402 39.130 8.56 0.00 0.00 3.16
3476 11121 4.426736 TTGTAAGGACCGAAGAACCTTT 57.573 40.909 0.00 0.00 42.83 3.11
3477 11122 5.549742 TTGTAAGGACCGAAGAACCTTTA 57.450 39.130 0.00 0.00 42.83 1.85
3478 11123 4.886579 TGTAAGGACCGAAGAACCTTTAC 58.113 43.478 0.00 0.00 42.83 2.01
3479 11124 3.413846 AAGGACCGAAGAACCTTTACC 57.586 47.619 0.00 0.00 40.54 2.85
3505 11150 1.534595 CCTCTGTTCAAGCAGTTCTGC 59.465 52.381 15.88 15.88 37.70 4.26
3552 11197 8.961294 ATAATCTTTCTTTGTCTCTCAGGATG 57.039 34.615 0.00 0.00 37.54 3.51
3607 11252 1.673168 ATTTCGATCTTGGCCTCAGC 58.327 50.000 3.32 0.00 38.76 4.26
3642 11287 3.321111 TGTGACTGTACTCTTCAGAACCC 59.679 47.826 0.00 0.00 36.81 4.11
3690 11336 0.800012 TTATTTTCGACGCCTGCCAC 59.200 50.000 0.00 0.00 0.00 5.01
3697 11343 1.450312 GACGCCTGCCACTGCTATT 60.450 57.895 0.00 0.00 38.71 1.73
3699 11345 0.609131 ACGCCTGCCACTGCTATTTT 60.609 50.000 0.00 0.00 38.71 1.82
3700 11346 0.099436 CGCCTGCCACTGCTATTTTC 59.901 55.000 0.00 0.00 38.71 2.29
3701 11347 0.099436 GCCTGCCACTGCTATTTTCG 59.901 55.000 0.00 0.00 38.71 3.46
3702 11348 1.737838 CCTGCCACTGCTATTTTCGA 58.262 50.000 0.00 0.00 38.71 3.71
3703 11349 1.398390 CCTGCCACTGCTATTTTCGAC 59.602 52.381 0.00 0.00 38.71 4.20
3704 11350 1.061131 CTGCCACTGCTATTTTCGACG 59.939 52.381 0.00 0.00 38.71 5.12
3705 11351 0.247695 GCCACTGCTATTTTCGACGC 60.248 55.000 0.00 0.00 33.53 5.19
3706 11352 0.373716 CCACTGCTATTTTCGACGCC 59.626 55.000 0.00 0.00 0.00 5.68
3707 11353 1.359848 CACTGCTATTTTCGACGCCT 58.640 50.000 0.00 0.00 0.00 5.52
3708 11354 1.061131 CACTGCTATTTTCGACGCCTG 59.939 52.381 0.00 0.00 0.00 4.85
3709 11355 0.026803 CTGCTATTTTCGACGCCTGC 59.973 55.000 0.00 0.00 0.00 4.85
3710 11356 1.352056 GCTATTTTCGACGCCTGCC 59.648 57.895 0.00 0.00 0.00 4.85
3711 11357 1.366111 GCTATTTTCGACGCCTGCCA 61.366 55.000 0.00 0.00 0.00 4.92
3712 11358 0.373716 CTATTTTCGACGCCTGCCAC 59.626 55.000 0.00 0.00 0.00 5.01
3713 11359 0.036765 TATTTTCGACGCCTGCCACT 60.037 50.000 0.00 0.00 0.00 4.00
3714 11360 1.577328 ATTTTCGACGCCTGCCACTG 61.577 55.000 0.00 0.00 0.00 3.66
3717 11363 4.435436 CGACGCCTGCCACTGCTA 62.435 66.667 0.00 0.00 38.71 3.49
3718 11364 2.187946 GACGCCTGCCACTGCTAT 59.812 61.111 0.00 0.00 38.71 2.97
3719 11365 1.450312 GACGCCTGCCACTGCTATT 60.450 57.895 0.00 0.00 38.71 1.73
3720 11366 1.002134 ACGCCTGCCACTGCTATTT 60.002 52.632 0.00 0.00 38.71 1.40
3721 11367 1.308069 ACGCCTGCCACTGCTATTTG 61.308 55.000 0.00 0.00 38.71 2.32
3751 11398 4.280929 GCCTAAAACCTGAACCAAATGACT 59.719 41.667 0.00 0.00 0.00 3.41
3763 11411 5.104259 ACCAAATGACTGACCCTATCTTC 57.896 43.478 0.00 0.00 0.00 2.87
3871 11522 1.924731 ACGAGAAGGAGGATGACACA 58.075 50.000 0.00 0.00 0.00 3.72
3909 11560 2.110967 CGCGAAGGGAGACGTAGGA 61.111 63.158 0.00 0.00 46.37 2.94
3910 11561 1.445716 CGCGAAGGGAGACGTAGGAT 61.446 60.000 0.00 0.00 46.37 3.24
3911 11562 0.311477 GCGAAGGGAGACGTAGGATC 59.689 60.000 0.00 0.00 0.00 3.36
3912 11563 1.970092 CGAAGGGAGACGTAGGATCT 58.030 55.000 0.00 0.00 0.00 2.75
3926 11592 2.893637 AGGATCTTCACATTTCGGACG 58.106 47.619 0.00 0.00 0.00 4.79
3938 11604 3.507009 CGGACGGTCTCGGTCCTC 61.507 72.222 19.02 1.25 41.39 3.71
4060 11726 4.480541 CTTTGTGTTGTTTGTGTGCTGTA 58.519 39.130 0.00 0.00 0.00 2.74
4286 13305 5.577554 ACACAAAAATACAAAAACGGGTCAC 59.422 36.000 0.00 0.00 0.00 3.67
4303 13322 3.120511 GGTCACGAACTCTTGAATTCTGC 60.121 47.826 7.05 0.00 0.00 4.26
4312 13331 6.059787 ACTCTTGAATTCTGCAGGTTAGAT 57.940 37.500 15.13 0.00 0.00 1.98
4317 13336 4.751600 TGAATTCTGCAGGTTAGATATGCG 59.248 41.667 15.13 0.00 42.92 4.73
4386 13405 9.438291 GATGGAATTTTTCATCAACATAGTACG 57.562 33.333 6.69 0.00 39.47 3.67
4428 13447 3.993658 ACTGGGACCTCCTATATGACA 57.006 47.619 0.00 0.00 36.20 3.58
4495 13514 2.282783 GGCCGGCCCAATCTGTTTT 61.283 57.895 36.64 0.00 0.00 2.43
4556 13576 3.857052 AGAGTTGCGACGGAATTTGATA 58.143 40.909 4.74 0.00 0.00 2.15
4700 13727 6.899393 ATAGTGAGAAGTTTTGAAATGCCA 57.101 33.333 0.00 0.00 0.00 4.92
4708 13735 5.655893 AGTTTTGAAATGCCACAATTTCG 57.344 34.783 5.47 0.00 45.55 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
345 348 4.451150 GTCCGTGCGCCAGATCCA 62.451 66.667 4.18 0.00 0.00 3.41
603 7573 1.457303 CTGAACAGTTCTTTCCGCTCG 59.543 52.381 14.51 0.00 0.00 5.03
604 7574 1.801178 CCTGAACAGTTCTTTCCGCTC 59.199 52.381 14.51 0.00 0.00 5.03
605 7575 1.416401 TCCTGAACAGTTCTTTCCGCT 59.584 47.619 14.51 0.00 0.00 5.52
606 7576 1.878953 TCCTGAACAGTTCTTTCCGC 58.121 50.000 14.51 0.00 0.00 5.54
607 7577 3.728845 TCTTCCTGAACAGTTCTTTCCG 58.271 45.455 14.51 1.30 0.00 4.30
690 7661 2.011046 GCATGCTCTGGGTCAAGTCTC 61.011 57.143 11.37 0.00 0.00 3.36
708 7679 1.132453 CGAAGACTCCACGTAGATGCA 59.868 52.381 0.00 0.00 0.00 3.96
758 7729 1.079405 GTGGCGAATGGGAAGACGA 60.079 57.895 0.00 0.00 0.00 4.20
763 7734 2.361104 GGCTGTGGCGAATGGGAA 60.361 61.111 0.00 0.00 39.81 3.97
988 7984 1.834822 CCGTCATCCTCCTCCTCCC 60.835 68.421 0.00 0.00 0.00 4.30
991 7987 2.444895 GCCCGTCATCCTCCTCCT 60.445 66.667 0.00 0.00 0.00 3.69
1110 8131 1.193462 CCCCAGCCCAAAAATCAGCA 61.193 55.000 0.00 0.00 0.00 4.41
1114 8135 1.948721 CTCGCCCCAGCCCAAAAATC 61.949 60.000 0.00 0.00 34.57 2.17
1150 8176 1.136695 TGAAACAGCTGCAAAACCCAG 59.863 47.619 15.27 0.00 0.00 4.45
1216 8243 7.800300 AGAATTACCTGAGTACTCTTCCTTT 57.200 36.000 23.01 10.09 0.00 3.11
1268 8295 1.532604 ATCCGAACCAGACGAGCACA 61.533 55.000 0.00 0.00 0.00 4.57
1274 8301 0.101399 CCAGAGATCCGAACCAGACG 59.899 60.000 0.00 0.00 0.00 4.18
1290 8317 1.759445 CTACACCCACAGATCTCCCAG 59.241 57.143 0.00 0.00 0.00 4.45
1293 8320 0.103208 CGCTACACCCACAGATCTCC 59.897 60.000 0.00 0.00 0.00 3.71
1300 8327 0.830444 AGAACTCCGCTACACCCACA 60.830 55.000 0.00 0.00 0.00 4.17
1308 8335 4.037327 CAGATCAGATTCAGAACTCCGCTA 59.963 45.833 0.00 0.00 0.00 4.26
1353 8432 3.431912 CACACTCGAATCGGATTTCACAA 59.568 43.478 4.47 0.00 0.00 3.33
1411 8490 1.974236 AGGACAGTTGAGCAGCTAACT 59.026 47.619 0.00 3.20 37.61 2.24
1438 8517 6.293649 AGGGTTATATGTTTTGGATCCCAT 57.706 37.500 9.90 7.86 35.31 4.00
1441 8520 6.008331 GGGTAGGGTTATATGTTTTGGATCC 58.992 44.000 4.20 4.20 0.00 3.36
1603 8761 2.435372 TCAAACCCAGTTCAACTGCT 57.565 45.000 12.49 0.00 44.63 4.24
1604 8762 3.186909 GTTTCAAACCCAGTTCAACTGC 58.813 45.455 12.49 0.00 44.63 4.40
1627 8832 1.163420 TTGTGGGCACAACTGCTACG 61.163 55.000 0.00 0.00 45.42 3.51
1745 8955 3.247173 GCTGCACTATGCTTCTGTCATAC 59.753 47.826 2.02 0.00 45.31 2.39
1751 8961 1.088340 AGCGCTGCACTATGCTTCTG 61.088 55.000 10.39 0.00 45.31 3.02
1848 9102 0.602562 TAGGCGCTGCATTTTGCTTT 59.397 45.000 7.64 0.00 45.31 3.51
1887 9141 9.410556 AGTTGCAAATTACATGATTTTACAGTC 57.589 29.630 0.00 0.00 0.00 3.51
1936 9402 5.120208 CAGTACGGAAATAACAGGACACAAG 59.880 44.000 0.00 0.00 0.00 3.16
1993 9517 8.752766 AAACAATGCAGATCAACAAAGAATAG 57.247 30.769 0.00 0.00 0.00 1.73
1995 9519 6.647895 GGAAACAATGCAGATCAACAAAGAAT 59.352 34.615 0.00 0.00 0.00 2.40
2005 9529 2.424956 GACCTGGGAAACAATGCAGATC 59.575 50.000 0.00 0.00 0.00 2.75
2061 9692 2.304180 ACAGGAAATGGAGTCAGACAGG 59.696 50.000 2.66 0.00 0.00 4.00
2160 9796 1.998315 CACTCTTCTCGTGCTTCCATG 59.002 52.381 0.00 0.00 0.00 3.66
2593 10229 0.107945 CTTTGCTCTTCTCCTCCCCG 60.108 60.000 0.00 0.00 0.00 5.73
2905 10543 1.562008 TCTTCACACTTGGGGTTGTCA 59.438 47.619 0.00 0.00 0.00 3.58
2974 10616 0.527565 CATGCCACTTGCCCTTGTAC 59.472 55.000 0.00 0.00 40.16 2.90
3296 10941 5.880054 AATGTACGGAAAACATCAGAAGG 57.120 39.130 0.00 0.00 36.56 3.46
3411 11056 1.871080 AGAATGGAATGTCGGCGATC 58.129 50.000 14.79 6.66 0.00 3.69
3476 11121 2.563179 GCTTGAACAGAGGAGACAGGTA 59.437 50.000 0.00 0.00 0.00 3.08
3477 11122 1.346068 GCTTGAACAGAGGAGACAGGT 59.654 52.381 0.00 0.00 0.00 4.00
3478 11123 1.345741 TGCTTGAACAGAGGAGACAGG 59.654 52.381 0.00 0.00 0.00 4.00
3479 11124 2.036992 ACTGCTTGAACAGAGGAGACAG 59.963 50.000 0.00 0.00 40.25 3.51
3534 11179 7.679783 TCAATAACATCCTGAGAGACAAAGAA 58.320 34.615 0.00 0.00 0.00 2.52
3538 11183 6.857437 TCTCAATAACATCCTGAGAGACAA 57.143 37.500 0.00 0.00 40.44 3.18
3539 11184 6.127225 CCTTCTCAATAACATCCTGAGAGACA 60.127 42.308 1.69 0.00 44.69 3.41
3545 11190 5.280499 TCTCCCTTCTCAATAACATCCTGA 58.720 41.667 0.00 0.00 0.00 3.86
3552 11197 5.091261 TGCTTCTCTCCCTTCTCAATAAC 57.909 43.478 0.00 0.00 0.00 1.89
3607 11252 2.460330 GTCACAAGGATGACAGCGG 58.540 57.895 1.08 0.00 46.89 5.52
3642 11287 3.479255 GCTTCTTGCCACCGAAAAG 57.521 52.632 0.00 0.00 35.15 2.27
3690 11336 0.026803 GCAGGCGTCGAAAATAGCAG 59.973 55.000 0.00 0.00 0.00 4.24
3697 11343 2.664851 CAGTGGCAGGCGTCGAAA 60.665 61.111 0.00 0.00 0.00 3.46
3700 11346 3.723235 ATAGCAGTGGCAGGCGTCG 62.723 63.158 5.53 0.00 44.61 5.12
3701 11347 1.026718 AAATAGCAGTGGCAGGCGTC 61.027 55.000 5.53 0.00 44.61 5.19
3702 11348 1.002134 AAATAGCAGTGGCAGGCGT 60.002 52.632 5.53 0.00 44.61 5.68
3703 11349 1.430632 CAAATAGCAGTGGCAGGCG 59.569 57.895 5.53 0.00 44.61 5.52
3704 11350 1.140375 GCAAATAGCAGTGGCAGGC 59.860 57.895 3.00 3.00 44.61 4.85
3721 11367 1.247567 TCAGGTTTTAGGCAAGCAGC 58.752 50.000 0.00 0.00 44.65 5.25
3751 11398 1.292242 AGGAGGCAGAAGATAGGGTCA 59.708 52.381 0.00 0.00 0.00 4.02
3791 11439 0.678048 GGCTTCTTGACCTCGGCAAT 60.678 55.000 0.00 0.00 0.00 3.56
3853 11501 2.611518 GTTGTGTCATCCTCCTTCTCG 58.388 52.381 0.00 0.00 0.00 4.04
3857 11505 0.321653 GCGGTTGTGTCATCCTCCTT 60.322 55.000 0.00 0.00 0.00 3.36
3904 11555 3.797256 CGTCCGAAATGTGAAGATCCTAC 59.203 47.826 0.00 0.00 0.00 3.18
3909 11560 2.233922 AGACCGTCCGAAATGTGAAGAT 59.766 45.455 0.00 0.00 0.00 2.40
3910 11561 1.616865 AGACCGTCCGAAATGTGAAGA 59.383 47.619 0.00 0.00 0.00 2.87
3911 11562 1.993370 GAGACCGTCCGAAATGTGAAG 59.007 52.381 0.00 0.00 0.00 3.02
3912 11563 1.667756 CGAGACCGTCCGAAATGTGAA 60.668 52.381 0.00 0.00 0.00 3.18
3926 11592 2.168666 AAAAGGCGAGGACCGAGACC 62.169 60.000 0.00 0.00 41.76 3.85
3938 11604 1.069906 CGAGGAGTTCACAAAAAGGCG 60.070 52.381 0.00 0.00 0.00 5.52
4060 11726 3.957497 AGATCACTTCTAGCTGATTCCGT 59.043 43.478 0.00 0.00 30.96 4.69
4286 13305 3.070018 ACCTGCAGAATTCAAGAGTTCG 58.930 45.455 17.39 0.00 33.02 3.95
4288 13307 5.869579 TCTAACCTGCAGAATTCAAGAGTT 58.130 37.500 17.39 9.73 0.00 3.01
4289 13308 5.489792 TCTAACCTGCAGAATTCAAGAGT 57.510 39.130 17.39 0.00 0.00 3.24
4290 13309 7.307870 GCATATCTAACCTGCAGAATTCAAGAG 60.308 40.741 17.39 3.80 35.96 2.85
4291 13310 6.484643 GCATATCTAACCTGCAGAATTCAAGA 59.515 38.462 17.39 10.00 35.96 3.02
4303 13322 9.295214 CTGAAATCTATACGCATATCTAACCTG 57.705 37.037 0.00 0.00 0.00 4.00
4386 13405 0.398098 TCACTACCGGGGGAGGATTC 60.398 60.000 6.32 0.00 34.73 2.52
4556 13576 4.008933 GCTGCAGGAGGTCGTGGT 62.009 66.667 17.12 0.00 32.80 4.16
4754 13781 7.062848 GCAGGATTTGTTCGTGTTTAATTTTG 58.937 34.615 0.00 0.00 41.32 2.44



Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.